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Yorodumi- PDB-5dx8: Crystal structure of CARM1, sinefungin, and methylated PABP1 pept... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dx8 | ||||||
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Title | Crystal structure of CARM1, sinefungin, and methylated PABP1 peptide (R455) | ||||||
Components |
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Keywords | TRANSFERASE / protein-substrate ternary complex | ||||||
Function / homology | Function and homology information negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / histone H3R17 methyltransferase activity / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / histone H3R2 methyltransferase activity / type I protein arginine methyltransferase / negative regulation of dendrite development / protein-arginine omega-N asymmetric methyltransferase activity ...negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / histone H3R17 methyltransferase activity / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / histone H3R2 methyltransferase activity / type I protein arginine methyltransferase / negative regulation of dendrite development / protein-arginine omega-N asymmetric methyltransferase activity / histone arginine N-methyltransferase activity / protein methyltransferase activity / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal / protein-arginine N-methyltransferase activity / positive regulation of cytoplasmic translation / M-decay: degradation of maternal mRNAs by maternally stored factors / poly(A) binding / regulatory ncRNA-mediated gene silencing / mRNA stabilization / poly(U) RNA binding / positive regulation of epithelial cell apoptotic process / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of fat cell differentiation / Translation initiation complex formation / histone methyltransferase activity / positive regulation of transcription by RNA polymerase I / cell leading edge / nuclear replication fork / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of viral genome replication / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / lysine-acetylated histone binding / response to cAMP / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / catalytic step 2 spliceosome / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / AUF1 (hnRNP D0) binds and destabilizes mRNA / mRNA 3'-UTR binding / PPARA activates gene expression / Heme signaling / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / Cytoprotection by HMOX1 / RMTs methylate histone arginines / Regulation of expression of SLITs and ROBOs / beta-catenin binding / mRNA splicing, via spliceosome / cytoplasmic stress granule / cytoplasmic ribonucleoprotein granule / Circadian Clock / lamellipodium / DNA-binding transcription factor binding / methylation / Estrogen-dependent gene expression / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / ribonucleoprotein complex / focal adhesion / mRNA binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.94 Å | ||||||
Authors | Boriack-Sjodin, P.A. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2016 Title: Structural Insights into Ternary Complex Formation of Human CARM1 with Various Substrates. Authors: Boriack-Sjodin, P.A. / Jin, L. / Jacques, S.L. / Drew, A. / Sneeringer, C. / Scott, M.P. / Moyer, M.P. / Ribich, S. / Moradei, O. / Copeland, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dx8.cif.gz | 292 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dx8.ent.gz | 245.7 KB | Display | PDB format |
PDBx/mmJSON format | 5dx8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dx8_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5dx8_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5dx8_validation.xml.gz | 53.1 KB | Display | |
Data in CIF | 5dx8_validation.cif.gz | 74.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/5dx8 ftp://data.pdbj.org/pub/pdb/validation_reports/dx/5dx8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39623.121 Da / Num. of mol.: 4 / Fragment: catalytic domain (UNP residues 134-479) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CARM1, PRMT4 / Plasmid: pFastBac / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q86X55, Transferases; Transferring one-carbon groups; Methyltransferases, EC: 2.1.1.125 #2: Protein/peptide | Mass: 1937.315 Da / Num. of mol.: 4 / Fragment: UNP residues 449-466 Mutation: Nterminal biotin and aminohexanoic acid, methylated R455 and R460 Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P11940 #3: Chemical | ChemComp-SFG / #4: Water | ChemComp-HOH / | Sequence details | The N-terminal of PABP1 peptide is modified with biotin and aminohexanoic acid. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M Ammonium Sulfate, 0.1 M Tris pH 8.5, 18% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 24, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→50 Å / Num. obs: 103564 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.94→2.06 Å / Rmerge(I) obs: 0.771 / Mean I/σ(I) obs: 2.6 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Resolution: 1.94→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.215 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.65 Å2 / Biso mean: 26.083 Å2 / Biso min: 8.98 Å2
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Refinement step | Cycle: final / Resolution: 1.94→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.941→1.992 Å / Total num. of bins used: 20
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